Main
James Sacco
Bioinformatics Scientist
Department of Gene and Cell Therapy
ASC Therapeutics
Milpitas, CA 95035
Independent, self-motivated bioinformatics scientist, with six years of combined experience in cancer immunotherapy and gene therapy. Specialist in computational biology of CRISPR gene editing. An analytical thinker and quick learner, with experience in next-generation sequencing (NGS) methods, such as RNA-Seq, and development of reproducible, robust pipelines.
Integrated genotype-phenotype data to predict disease severity. Developed machine learning applications to analyze population-scale genomics and real-world patient data.
Experience
Bioinformatics Scientist
ASC Therapeutics (Contract)
Milpitas, CA
Present - 2021
● Quantify and characterize CRISPR gene modifications, with both custom and open-source tools for genomic data analysis.
● Query, retrieve, and integrate data from public genomics databases, to enhance on-target gene editing with sequence alignment protocols.
● Examine concordance and sensitivity of five open-source CRISPR off-target detection methods (CALITAS, CHANGE-Seq, CRISPResso, GUIDE-Seq, and Cas-OFFinder).
● Streamline high-performance analyses for bench scientists by constructing custom data pipelines, command line tools, and user interfaces.
● Generate reproducible reports for publication-quality manuscripts.
Biomarker Data Analyst II
Genentech (Contract)
South San Francisco, CA
2020 - 2019
● Established department-first machine learning pipeline to study effects of biomarker operations on quality of cancer immunotherapy assays.
● Upgraded data operations for six data streams, including flow cytometry, biomarker operations, and oncology data warehouses.
● Monitored and solved sample data quality issues for two cancer immunotherapy trial arms.
Data Curator
Genentech (Contract)
South San Francisco, CA
2019 - 2018
PROGRAMMING SKILLS
R
Python
Linux
Git
GitHub
Markdown
Dash
C++
MATLAB
● Collaborated with AI engineers to create an ETL pipeline for multi-modal survival prediction and patient stratification, by using Python ML and R to integrate gene panel and RNA-Seq data.
● Designed ETL data pipeline for integration of real-world EHRs into deep learning module, using Python, SQL, and Apache Spark.
● Organized and managed close coordination of Artificial Intelligence, data management, and DevOps functions, to bring clinical machine learning from prototype to production.
Data Curator, Bioinformatics Analyst
BioMarin Pharmaceutical (Contract)
San Rafael, CA
2018 - 2017
● Established an integrated genetic and curated literature workflow to predict incidence and prevalence rates of over sixty rare, genetic disorders, with statistical and data visualization R packages (ggplot2) and MATLAB.
● Upgraded and tested RNA-Seq data pipeline (STAR2, SAMtools, Bioconductor) to discern disease contribution of rare variants to neural disease.
● Spearheaded development of three relational databases derived from Hail population genomics platform, in collaboration with software engineer.
● Co-authored manuscript submitted to peer-reviewed publication, on prediction of disease severity in metachromatic leukodystrophy.
● Developed allele-specific association models and GWAS analysis software for two later published manuscripts.
Research Associate
Pearse Lab: The Miami Project to Cure Paralysis, The Miller School of Medicine, University of Miami
Miami, FL
2017 - 2016
● Mentored research associates in developing bioinformatic skills, specifically in multiple sequence alignment and standard molecular biological protocols (restriction enzyme digestion, gel electrophoresis, spectrophotometry).
● Identified over forty putative conserved vertebrate phosphodiesterase proteins, by using multiple sequence alignment and genomic evidence.
Education
Rowan University, Graduate School of Biomedical Sciences
Master of Biomedical Science (Distinction)
Stratford, NJ
N/A
“Hippocampal long-term potentiation in neurodegenerative disorders”
Florida International University, The Honors College
BSc, Biological Sciences
Miami, FL
Professional Development
I have participated in bioinformatics and software workshops and Meetup.com groups, in both Seattle, WA and San Francisco, CA, including:
SF/Bay AI Developers Group
San Jose Data Science and AI/ML Meetup
Hacker Dojo
Seattle Sequencing
LANGUAGES
English: Native
Spanish: Bilingual Proficiency
Bulk and Single Cell Transcriptomics Training Program
Pine Biotech, Tauber Bioinformatics Research Center
Online
2022
Publications
Regulating Axonal Responses to Injury: The Intersection between Signaling Pathways Involved in Axon Myelination and The Inhibition of Axon Regeneration.
Frontiers in Molecular Neuroscience. 2016 Jun 8;9:33.
N/A
2016
Rao S.N., Pearse D.D. Manuscript Editor
Conference Papers
Prediction of disease severity in metachromatic leukodystrophy using measures of protein activity and a novel phenotype matrix.
American Society of Human Genetics Virtual Meeting. [Poster] [Forthcoming on bioRxiv.org]
Online
2020
Trinidad M., Hong X., Sacco J., Nguyen H.P., Clark W.T., Froelich S., LeBowitz J.H., Gelb M.H.
Association of HGMD and gnomAD variants of unknown significance with prediction of disease incidence and prevalence.
BioMarin Internal Research and Development Asilomar Conference. [Poster]
Pacific Grove, CA
2018
Sacco J., Clark W.T., Yu K., Wu K., LeBowitz J.H.
Research Projects
Characterization of glycan substrates accumulating in GM1 gangliosidosis
Molecular Genetics and Metabolism Reports. 2019. 21, p.100524.
N/A
2019
Lawrence R., et al.
Phosphodiesterase Inhibitors as a Therapeutic Approach to Neuroprotection and Repair
International Journal of Molecular Sciences. 2017. 18(4): 696.
N/A
2017
Knott E.P., et al.
Presentations
Data Visualization of RNA-Seq Differential Expression Analysis with DESeq2
Doudna Lab: Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley
Berkeley, CA
2022
Topics: Introduction to RNA-Seq, Standard Workflows with DESeq2, Reference-Based Assembly, Exploratory Data Analysis, Statistical Analysis, Data Visualization, Gene Set Enrichment, Variant Annotation
● Presented publication-quality RNA-Seq data summaries and representations to post-doctoral associates
Teaching
Peer-Led Team Learning
Florida International University
Miami, FL
2009
General Biology II facilitator for two concurrent PLTL courses
Disclaimer
Made with 💘 using R pagedown.
Last update: 2022-02-14.The most recent version of this resume is available here.